Soybean (Glycine max L. Merr) is a major cash crop in North America and around the globe. Soybean oil is one of the most widely used edible oils, and soybeans are used worldwide as animal feed and for human consumption and for industrial purposes. P. sojae is an oomycete pathogen, which was first described in Ohio and shortly thereafter in Indiana and North Carolina (Suhovecky and Schmitthenner, Ohio Farm Home Res. 40:85-86 (1955)). P. sojae has now been reported to be present in all soybean growing regions of the U.S. as well as other parts of the world (Zhang et al. MPMI. 19(12):1302-1310(2006); (Wrather et al. Can. J. Plant Pathol. 23:115-121 (2001)). Symptoms of Phytophthora Root Rot (PRR) caused by P. sojae include yellowing and wilting of leaves and browning of lower stems and branches (Demirbas et al. Crop Sci. 41:1220-1227 (2001)). PRR is the second leading cause of yield loss in soybean in the United States. In 1998, yield losses due to PRR, in the U.S. and Argentina, the top soybean producing countries, were 1149 and 92 thousand metric tons respectively (Id.). PRR results in annual worldwide soybean crop losses of S1 to S2 billion (Zhang et al. MPMI. 19(12):1302-1310(2006)).
To date, eight loci, Rps1, Rps2, Rps3, Rps4, Rps5, Rps6, Rps7, and Rps8, have been identified which provide race-specific resistance to P. sojae. These loci were mapped to chromosomes 3, 16, 13, 18, 18, 18, 3 and 13 (previously called molecular linkage groups (MLG) N, J, F, G, G, G, N, and F, respectively) and simple sequence repeat (SSR) markers were reported to be linked to these genes (Burnham et al. Crop Sci. 43:101-105 (2003)); Diers et al. Crop Sci. 32:377-383 (1992); Gordon et al. Crop Sci. 46:168-173 (2005); Gordon et al. Phytopathology 97:113-118 (2007); Lohnes and Schmitthenner, Crop Sci. 37:555-556 (1997); Sandhu et al. Genetics 168:2157-2167 (2004); Sandhu et al. J. Hered. 96(5):536-541 (2005); Weng et al. J. Hered. 92:442-446 (2001)).
The Rps1 locus is complex having multiple alleles including Rps1a, Rps1b, Rps1c, Rps1d, and Rps1k (Bernard and Cremeens, Soybean Genet. Newsletter 8:40-42 (1981); Lohnes and Schmitthenner, Crop Sci. 37:555-556 (1997); Ferro et al., Crop Sci. 46:2427-2436 (2006); Weng et al. J. Hered. 92:442-446 (2001)). Rps1a was mapped on chromosome 3 (previously called MLG N), flanked by SSR markers, Satt159 (0.7 cM) and Satt009 (3.2 cM) (Weng et al. J. Hered. 92:442-446 (2001)). The recombination value was reported to be 0.16 and 0.13 between the gene Rps1 and Satt159 and Satt152 in another research (Demirbas et al. Crop Sci. 41:1220-1227 (2001)). Additionally, Satt530 and Satt584 were also reported to be linked to Rps1, Rps1b, and Rps1c with recombination values of 0.00 and 0.00, 0.12 and 0.20, and 0.14 and 0.21, respectively (Id.).
Rps1-k, first identified in the cultivar Kingwa (Bernard and Cremeens Soybean Genet. Newsletter 8:40-42 (1981)), has been used extensively used gene in breeding Phytophthora-resistant soybean cultivars (Schmitthenner et al., Plant Dis. 78:269-276(1994)). High resolution genetic and physical maps have been constructed for the Rps1-k region, and the gene has been isolated through positional cloning and transformation experiments and its sequence has been published in GenBank with the accession EU450800 (Bhattacharyya et al. Plant Mol. Biol. 34:255-264 (1997); Gao et al. Mol. Plant Microbe Interact. 18:1035-1045 (2005); Kasuga et al. Mol. Plant Microbe Interact. 10:1035-1044 (1997)). Although previously Rps1-k was considered to be a single gene, two functional units/genes, Rps1-k-1 and Rps1-k-2 were cloned from the Rps1-k locus. Rps1-k-1 is located between 17988 bp to 21677 bp and Rps1-k-2 is located between 42421 bp to 46170 bp of the GenBank accession EU450800. The Rps1-k gene sequences are disclosed in U.S. Pat. No. 7,256,323B1 to Bhattacharyya et al.
Currently, the presence or absence of Rps1 alleles is determined by phenotyping against different races of P. sojae in the greenhouse. Thus, the present invention overcomes the shortcomings in the art by providing markers associated with the different Rps1 alleles, thereby allowing for a more precise and faster characterization of soybean cultivars for the presence or absence Rps1 alleles by molecular analysis rather than by more time consuming greenhouse phenotypic analysis.